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lespernater/README.md

Hi πŸ‘‹

I'm Nate β€” AI engineer and bioinformatics researcher specializing in machine learning and intelligent systems for ecological and genomic analysis.


Programming Languages:

Python R Bash SQL

Development & Tooling

Git HPC uv Docker

Artificial Intelligence and Machine Learning:

PyTorch TensorFlow HuggingFace scikit-learn OpenAI Anthropic

Scientific Computing and Bioinformatics:

NumPy pandas Biopython Bioconductor Nextflow matplotlib ggplot2

Data Engineering and Web:

FastAPI SQLite Streamlit Flask Quarto


Work I Enjoy

πŸ”­ Building agentic AI systems and custom MCP servers for scientific data analysis

🧬 Developing deep learning architectures for multi-omics research in medicine and biodiversity

🌱 Exploring the intersection of machine learning, genomics, and biodiversity informatics

πŸ“Š Creating tools that democratize sophisticated data analysis for domain experts


Recent Highlights

MCP Server & Agentic AI Systems Development - Custom Model Context Protocol server connecting LLMs to 40M+ phenology observations; Autonomous agentic data analysis workflows in phenology - Vector Institute & USA National Phenology Network

Deep Learning for Genomics - Novel deep learning architecture achieving improved accuracy for viral detection in metagenomic sequences compared to Kraken2 - CFIA (GigaScience, Aug 2025)

Vision-Language Models + RAG - Taxonomic classification for rare arthropod species pairing image captioning with RAG - MLRG, CBG & ABC (Canadian AI Conference, May 2025)


Past Collaborations

  • University of Guelph's Machine Learning Research Group (MLRG)
  • Vector Institute for Artificial Intelligence
  • USA National Phenology Network (USA-NPN)
  • Canadian Food Inspection Agency (CFIA)
  • Centre for Biodiversity Genomics (CBG)
  • AI and Biodiversity Change Global Centre (ABC)

πŸ“« Email πŸ’Ό LinkedIn

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  1. uoguelph-mlrg/taxonomic-rag-system uoguelph-mlrg/taxonomic-rag-system Public

    Code for "Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning with RAG for Interpretable Classification" - proceedings of the 38th Canadian Conference on Artificial Intelligence

    Python